[med-svn] [canu] branch upstream updated (c0aaa7a -> bce57ac)
Afif Elghraoui
afif at moszumanska.debian.org
Wed Jul 13 15:49:19 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch upstream
in repository canu.
from c0aaa7a Imported Upstream version 1.1+dfsg
new bce57ac Imported Upstream version 1.3+dfsg
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
README.md | 32 +-
addCopyrights-BuildData.pl | 10 +-
addCopyrights.dat | 3119 +++-----------------
addCopyrights.pl | 2 +-
documentation/source/commands/bogart.rst | 34 +-
.../source/commands/gatekeeperDumpFASTQ.rst | 1 +
documentation/source/commands/ovStoreDump.rst | 10 +-
documentation/source/conf.py | 4 +-
documentation/source/faq.rst | 124 +
documentation/source/index.rst | 2 +
documentation/source/parameter-reference.rst | 124 +-
documentation/source/quick-start.rst | 140 +-
documentation/source/tutorial.rst | 27 +-
src/AS_UTL/AS_UTL_stackTrace.C | 14 +-
src/AS_UTL/intervalList.H | 6 +-
.../Binomial_Bound.H => AS_UTL/intervalListTest.C} | 47 +-
src/AS_UTL/memoryMappedFile.H | 8 +-
src/AS_UTL/stddev.C | 41 -
src/AS_UTL/stddev.H | 92 +-
src/AS_UTL/stddevTest.C | 116 +
src/AS_global.H | 6 +
src/Makefile | 39 +-
src/bogart/AS_BAT_BestOverlapGraph.C | 1015 +++----
src/bogart/AS_BAT_BestOverlapGraph.H | 192 +-
src/bogart/AS_BAT_Breaking.C | 332 ---
src/bogart/AS_BAT_Breaking.H | 112 -
src/bogart/AS_BAT_ChunkGraph.C | 28 +-
src/bogart/AS_BAT_ChunkGraph.H | 14 +-
src/bogart/AS_BAT_Datatypes.H | 339 ---
src/bogart/AS_BAT_FragmentInfo.C | 18 +-
src/bogart/AS_BAT_FragmentInfo.H | 123 +
src/bogart/AS_BAT_Instrumentation.C | 494 +++-
src/bogart/AS_BAT_Instrumentation.H | 3 +-
src/bogart/AS_BAT_IntersectBubble.C | 660 -----
src/bogart/AS_BAT_IntersectBubble.H | 44 -
src/bogart/AS_BAT_IntersectSplit.C | 334 ---
src/bogart/AS_BAT_IntersectSplit.H | 151 -
src/bogart/AS_BAT_Joining.C | 405 ---
src/bogart/AS_BAT_Joining.H | 45 -
src/bogart/AS_BAT_Logging.C | 76 +-
src/bogart/AS_BAT_Logging.H | 17 +-
src/bogart/AS_BAT_MarkRepeatReads.C | 1133 +++++++
.../AS_BAT_MarkRepeatReads.H} | 20 +-
src/bogart/AS_BAT_MergeSplitJoin.C | 1763 -----------
src/bogart/AS_BAT_MergeSplitJoin.H | 57 -
src/bogart/AS_BAT_MergeUnitigs.C | 246 ++
.../AS_BAT_MergeUnitigs.H} | 18 +-
src/bogart/AS_BAT_Outputs.C | 490 +--
src/bogart/AS_BAT_Outputs.H | 17 +-
src/bogart/AS_BAT_OverlapCache.C | 67 +-
src/bogart/AS_BAT_OverlapCache.H | 70 +-
src/bogart/AS_BAT_PlaceContains.C | 279 +-
src/bogart/AS_BAT_PlaceContains.H | 11 +-
src/bogart/AS_BAT_PlaceFragUsingOverlaps.C | 501 +---
src/bogart/AS_BAT_PlaceFragUsingOverlaps.H | 13 +-
src/bogart/AS_BAT_PlaceZombies.C | 110 -
src/bogart/AS_BAT_PlaceZombies.H | 44 -
src/bogart/AS_BAT_PopBubbles.C | 679 +++++
.../SimpleAligner.H => bogart/AS_BAT_PopBubbles.H} | 21 +-
src/bogart/AS_BAT_PopBubbles.txt | 87 +
src/bogart/AS_BAT_PopulateUnitig.C | 54 +-
src/bogart/AS_BAT_PromoteToSingleton.C | 4 +-
.../AS_BAT_PromoteToSingleton.H} | 20 +-
src/bogart/AS_BAT_ReconstructRepeats.C | 15 +-
src/bogart/AS_BAT_RepeatJunctionEvidence.H | 232 --
src/bogart/AS_BAT_SetParentAndHang.C | 280 +-
src/bogart/AS_BAT_SetParentAndHang.H | 2 +
src/bogart/AS_BAT_SplitDiscontinuous.C | 52 +-
src/bogart/AS_BAT_Unitig.C | 505 +++-
src/bogart/AS_BAT_Unitig.H | 280 +-
src/bogart/AS_BAT_UnitigVector.C | 218 ++
src/bogart/AS_BAT_UnitigVector.H | 61 +
src/bogart/AS_BAT_Unitig_AddAndPlaceFrag.C | 144 -
src/bogart/AS_BAT_Unitig_AddFrag.C | 32 +-
src/bogart/AS_BAT_Unitig_PlaceFragUsingEdges.C | 561 +---
src/bogart/AS_BAT_findEdges.C | 178 --
src/bogart/bogart.C | 299 +-
src/bogart/bogart.mk | 13 +-
src/bogart/buildGraph.C | 324 +-
src/correction/errorEstimate.C | 206 ++
.../{readConsensus.mk => errorEstimate.mk} | 4 +-
src/falcon_sense/falcon_sense.C | 10 +-
src/falcon_sense/libfalcon/falcon.C | 19 +-
src/falcon_sense/libfalcon/falcon.H | 2 +-
src/falcon_sense/libfalcon/kmer_lookup.C | 0
src/main.mk | 4 +-
src/merTrim/merTrimAdapter.C | 0
src/meryl/libleaff/fastaFile.C | 3 -
src/meryl/libleaff/fastaStdin.C | 14 +-
src/meryl/libleaff/fastqFile.C | 4 -
src/meryl/libleaff/fastqStdin.C | 7 +-
src/meryl/libleaff/gkStoreFile.C | 2 +-
src/meryl/libleaff/seqCache.C | 3 -
src/meryl/libleaff/seqFile.H | 2 +
src/meryl/libmeryl.C | 125 +-
src/meryl/libmeryl.H | 7 +-
src/meryl/meryl-build.C | 65 +-
src/meryl/meryl-dump.C | 4 +-
src/mhap/mhap.mk | 4 +-
.../correctOverlaps-Correct_Frags.C | 13 +-
.../correctOverlaps-Prefix_Edit_Distance.C | 6 +-
.../correctOverlaps-Read_Olaps.C | 7 +
.../correctOverlaps-Redo_Olaps.C | 21 +-
src/overlapErrorAdjustment/correctOverlaps.C | 30 +
src/overlapErrorAdjustment/correctOverlaps.H | 6 +
.../findErrors-Analyze_Alignment.C | 30 +-
src/overlapErrorAdjustment/findErrors-Dump.C | 97 +
.../findErrors-Dump.mk} | 6 +-
src/overlapErrorAdjustment/findErrors.C | 8 +
.../overlapInCore-Process_String_Overlaps.C | 11 +-
src/overlapInCore/overlapInCore.C | 8 +-
src/overlapInCore/overlapInCore.H | 30 +-
src/overlapInCore/overlapPair.C | 27 +-
src/pipelines/bogart-sweep.pl | 185 ++
src/pipelines/canu.pl | 27 +-
src/pipelines/canu/Configure.pm | 118 +-
src/pipelines/canu/CorrectReads.pm | 30 +-
src/pipelines/canu/CorrectReads.txt | 41 +
src/pipelines/canu/Defaults.pm | 118 +-
src/pipelines/canu/ErrorEstimate.pm | 258 ++
src/pipelines/canu/Execution.pm | 103 +-
src/pipelines/canu/Execution.txt | 85 +
src/pipelines/canu/Gatekeeper.pm | 22 +-
src/pipelines/canu/Grid_LSF.pm | 9 +
src/pipelines/canu/Grid_PBSTorque.pm | 33 +-
src/pipelines/canu/Grid_SGE.pm | 11 +
src/pipelines/canu/Grid_Slurm.pm | 43 +-
src/pipelines/canu/HTML.pm | 144 +-
src/pipelines/canu/Meryl.pm | 44 +-
src/pipelines/canu/Output.pm | 8 +-
src/pipelines/canu/OverlapBasedTrimming.pm | 9 +-
src/pipelines/canu/OverlapErrorAdjustment.pm | 59 +-
src/pipelines/canu/OverlapInCore.pm | 13 +
src/pipelines/canu/OverlapMMap.pm | 77 +-
src/pipelines/canu/OverlapMhap.pm | 160 +-
src/pipelines/canu/OverlapStore.pm | 48 +-
src/pipelines/canu/Unitig.pm | 58 +-
src/stores/gatekeeperCreate.C | 6 +-
src/stores/gatekeeperDumpFASTQ.C | 90 +-
src/stores/gkStore.C | 24 +-
src/stores/gkStore.H | 10 +-
src/stores/gkStoreEncode.C | 4 +-
src/stores/ovOverlap.C | 19 +
src/stores/ovStore.H | 6 +
src/stores/ovStoreBuild.C | 103 +-
src/stores/ovStoreDump.C | 389 ++-
src/stores/ovStoreStats.C | 73 +-
src/stores/tgStoreCompress.C | 170 ++
.../{ovStoreSorter.mk => tgStoreCompress.mk} | 4 +-
src/stores/tgStoreCoverageStat.C | 66 +-
src/stores/tgStoreLoad.C | 6 +-
src/utgcns/libNDFalcon/dw.C | 0
src/utgcns/libNDFalcon/dw.H | 0
src/utgcns/libcns/NOTES | 38 +
src/utgcns/utgcns.C | 1 +
155 files changed, 9405 insertions(+), 11392 deletions(-)
create mode 100644 documentation/source/faq.rst
copy src/{overlapInCore/liboverlap/Binomial_Bound.H => AS_UTL/intervalListTest.C} (51%)
delete mode 100644 src/AS_UTL/stddev.C
create mode 100644 src/AS_UTL/stddevTest.C
delete mode 100644 src/bogart/AS_BAT_Breaking.C
delete mode 100644 src/bogart/AS_BAT_Breaking.H
delete mode 100644 src/bogart/AS_BAT_Datatypes.H
create mode 100644 src/bogart/AS_BAT_FragmentInfo.H
delete mode 100644 src/bogart/AS_BAT_IntersectBubble.C
delete mode 100644 src/bogart/AS_BAT_IntersectBubble.H
delete mode 100644 src/bogart/AS_BAT_IntersectSplit.C
delete mode 100644 src/bogart/AS_BAT_IntersectSplit.H
delete mode 100644 src/bogart/AS_BAT_Joining.C
delete mode 100644 src/bogart/AS_BAT_Joining.H
create mode 100644 src/bogart/AS_BAT_MarkRepeatReads.C
copy src/{utgcns/libpbutgcns/SimpleAligner.H => bogart/AS_BAT_MarkRepeatReads.H} (70%)
delete mode 100644 src/bogart/AS_BAT_MergeSplitJoin.C
delete mode 100644 src/bogart/AS_BAT_MergeSplitJoin.H
create mode 100644 src/bogart/AS_BAT_MergeUnitigs.C
copy src/{utgcns/libpbutgcns/SimpleAligner.H => bogart/AS_BAT_MergeUnitigs.H} (74%)
delete mode 100644 src/bogart/AS_BAT_PlaceZombies.C
delete mode 100644 src/bogart/AS_BAT_PlaceZombies.H
create mode 100644 src/bogart/AS_BAT_PopBubbles.C
copy src/{utgcns/libpbutgcns/SimpleAligner.H => bogart/AS_BAT_PopBubbles.H} (72%)
create mode 100644 src/bogart/AS_BAT_PopBubbles.txt
copy src/{utgcns/libpbutgcns/SimpleAligner.H => bogart/AS_BAT_PromoteToSingleton.H} (75%)
delete mode 100644 src/bogart/AS_BAT_RepeatJunctionEvidence.H
create mode 100644 src/bogart/AS_BAT_UnitigVector.C
create mode 100644 src/bogart/AS_BAT_UnitigVector.H
delete mode 100644 src/bogart/AS_BAT_Unitig_AddAndPlaceFrag.C
delete mode 100644 src/bogart/AS_BAT_findEdges.C
create mode 100644 src/correction/errorEstimate.C
copy src/correction/{readConsensus.mk => errorEstimate.mk} (90%)
mode change 100755 => 100644 src/falcon_sense/libfalcon/falcon.C
mode change 100755 => 100644 src/falcon_sense/libfalcon/falcon.H
mode change 100755 => 100644 src/falcon_sense/libfalcon/kmer_lookup.C
mode change 100755 => 100644 src/merTrim/merTrimAdapter.C
create mode 100644 src/overlapErrorAdjustment/findErrors-Dump.C
copy src/{correction/filterCorrectionOverlaps.mk => overlapErrorAdjustment/findErrors-Dump.mk} (75%)
create mode 100644 src/pipelines/bogart-sweep.pl
create mode 100644 src/pipelines/canu/CorrectReads.txt
create mode 100644 src/pipelines/canu/ErrorEstimate.pm
create mode 100644 src/pipelines/canu/Execution.txt
create mode 100644 src/stores/tgStoreCompress.C
copy src/stores/{ovStoreSorter.mk => tgStoreCompress.mk} (87%)
mode change 100755 => 100644 src/utgcns/libNDFalcon/dw.C
mode change 100755 => 100644 src/utgcns/libNDFalcon/dw.H
create mode 100644 src/utgcns/libcns/NOTES
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